please could you advise about the best BioC/R package to use for gene set enrichment analysis ;)
on a side note, may I ask the same question about the easiest package to use for survival analysis :)
have you tried the gsea package from the broad institute?
or the gage package
I recommend the GOseq package for GO enrichment analysis, it's quite easy in use if you read the manual first. You only need a list of your significant genes and a list of all your assayed genes.
thank you !
I'm a bit late for your question but I think the limma package must be mentioned: see the help pages for camera, roast and romer. These are gene set tests, not enrichment tests, i.e., no DEG list required.
thanks Axel !
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